If so, the answer is "yes". I may not understand what you mean by "use Quercus to run my PHP code on the JVM and call into my Java code", but it certainly sounds like it's bundled into your code. If you only need to have something that is a "PHP interpreter in Java" and can provide another one, you could probably have documentation stating "You can, if you want, use Quercus".

I think the real answer here is to consult a lawyer, specializing in electronic copyright.